Pelini is expected to be introduced at a news conference Monday.
Current Florida Atlantic coach Howard Schnellenberger, who announced in August that he is retiring at the end of this season, will coach his final game Saturday against Louisiana-Monroe.
FAU believes Pelini, the brother of Nebraska coach Bo Pelini, will bring discipline and organization, solid defense and effective recruiting. FAU is likely to employ a spread-based, up-tempo offense.
When Carl Pelini arrived at Nebraska in 2008, he inherited a defense that ranked 112th out of 119 teams nationally in yards allowed.
Under his direction, the Cornhuskers ranked 55th in total defense in 2008, seventh in 2009 and 11th in 2010. The defense is ranked 36th this season.
Although Carl Pelini is widely considered to be an outstanding recruiter, he has never been a head coach above the high school level. Before joining the Nebraska staff, he was an assistant coach at Ohio from 2005 to 2007; defensive coordinator at Division II Minnesota State in 2004; and a graduate assistant at Nebraska in 2003.
Nebraska athletic director Tom Osborne was among those who recommended Carl Pelini.
Among the other candidates FAU considered were Garrick McGee, Mike Stoops, Eddie Gran, Curtis Luper and Willie Martinez.
Joe Schad is a college football reporter for ESPN. Information from The Associated Press was used in this report.